miR-Intess™

candidate miRBase miRNAs

miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK (26 loci)

rno-mir-551b

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-551b 5arm	21	12	0	0	0	0	0	0	0	0
rno-mir-551b 3arm	4653	5897	10	7	8	18	4	6	13	4
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-551b 5arm	0.001	0.001	0	0	0	0	0	0	0	0
rno-mir-551b 3arm	0.155	0.257	0.001	0.000	0.000	0.001	0.000	0.000	0.001	0.000

sblock6427 (miRBase rno-mir-551b) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-551b

0.001

no

no

0.44/0.56

18/24/0.82

0.0 0.0

2.3 1.2

25 9635

0 0

2 10

0 0

17 20

1 7

5arm 3arm

1 1

nd nd

0.22 0.16

3 2

10653

10

5

3

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------CGACCCA-------------------------------------------	10414	novel
seed	------------------------------------------------------------------------------GACCCAU------------------------------------------	200	novel
seed	--------------------------------------AAAUCAA----------------------------------------------------------------------------------	33	novel
seed	-------------------------------------------------------------------------------ACCCAUA-----------------------------------------	4	novel
seed	---------------------------------------------------------------------------GGCGACC---------------------------------------------	1	novel
seed	----------------------------------------------------------------------------GCGACCC--------------------------------------------	1	miR-551b
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------------------------------------GCGACCCATACTTGGTTTCAGT-----------------------------	22	1451	1825	1	3	2	3	2	-	1	2
	----------------------------------------------------------------------------GCGACCCATACTTGGTTTCAG------------------------------	21	1301	1610	2	-	2	6	-	2	5	2
	----------------------------------------------------------------------------GCGACCCATACTTGGTTTCA-------------------------------	20	961	1210	1	3	1	5	-	3	6	-
	----------------------------------------------------------------------------GCGACCCATACTTGGTTTC--------------------------------	19	561	716	2	1	2	4	1	-	1	-
	----------------------------------------------------------------------------GCGACCCATACTTGGTTT---------------------------------	18	219	322	2	-	-	-	1	1	-	-
	----------------------------------------------------------------------------GCGACCCATACTTGGTTTCAGTG----------------------------	23	73	95	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------CGACCCATACTTGGTTTCAGT-----------------------------	21	44	53	2	-	1	-	-	-	-	-
	-----------------------------------------------------------------------------CGACCCATACTTGGTTTCAG------------------------------	20	20	23	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------CGACCCATACTTGGTTTCA-------------------------------	19	13	27	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------CGACCCATACTTGGTTTC--------------------------------	18	9	7	-	-	-	-	-	-	-	-
	-------------------------------------GAAATCAAGCTTGGGTGA------------------------------------------------------------------------	18	10	3	-	-	-	-	-	-	-	-
	-------------------------------------GAAATCAAGCTTGGGTGAGACCT-------------------------------------------------------------------	23	5	4	-	-	-	-	-	-	-	-
	-------------------------------------GAAATCAAGCTTGGGTGAGACC--------------------------------------------------------------------	22	3	2	-	-	-	-	-	-	-	-
	------------------------------------------------------------------------------GACCCATACTTGGTTTCA-------------------------------	18	-	4	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------------GCGACCCATACTTGGTTTCAGTGG---------------------------	24	-	3	-	-	-	-	-	-	-	-
	-------------------------------------GAAATCAAGCTTGGGTGAGAC---------------------------------------------------------------------	21	2	1	-	-	-	-	-	-	-	-
	-------------------------------------GAAATCAAGCTTGGGTGAGA----------------------------------------------------------------------	20	-	2	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------AGGCGACCCATACTTGGTTTCAG------------------------------	23	-	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------------GGCGACCCATACTTGGTT----------------------------------	18	-	1	-	-	-	-	-	-	-	-
	-------------------------------------GAAATCAAGCTTGGGTGAG-----------------------------------------------------------------------	19	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------CGACCCATACTTGGTTTCAGTG----------------------------	22	1	-	-	-	-	-	-	-	-	-
rno-miR-551b	---------------------------------------------------------------------------GGCGACCCATACTTGGTTTCAGT-----------------------------	23	-	-	-	-	-	-	-	-	-	-
rat	--------------------GTGCTCTTGTGGCCCATGAAATCAAGCTTGGGTGAGACCTGGTACAGAACAGGAAGGCGACCCATACTTGGTTTCAGTGGCTGCAAGAATGGCTCTAT---------
human	CTCTGTTAGATCTGCCAGATGTGCTCTCCTGGCCCATGAAATCAAGCGTGGGTGAGACCTGGTGCAGAACGGGAAGGCGACCCATACTTGGTTTCAGAGGCTGTGAGAATAACTGCAATTTAGAGGG
mouse	----------------------------------CATGAAATCAAGCTTGGGTGAGACCTGGTGCAGAACAGGAAGGCGACCCATACTTGGTTTCAGT-----------------------------
	************* *************** ****** **************************
	+++++                    ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++         +++++	ENSRNOT00000039603 ENSRNOG00000023908 NP_001101133.1
	.....                    >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         .....	ENSRNOT00000054541 ENSRNOG00000036429 rno-mir-551b
rat	(.(((((((..(((..((((((((((..((((((...((((........))))....).)))))..))))))))))..)))..)))))...)).)...	1.000 -43.40
human	((((.((((((.((.(((.(((..((((.(((((..((((((((((..((((((...((((........))))....)).))))..))))))))))..))))).))))))).)))))))))))))))	0.989 -47.80
mouse	..((((((((((..((((((...((((........))))....)).))))..))))))))))..	1.000 -25.60

rat	chromosome:2:114095878:114095975:1	Same_strand|Boundary_non-coding|ENSRNOT00000059022|ENSRNOG00000023908 ## Same_strand|Exonic_non-coding|ENSRNOT00000054541|ENSRNOG00000036429 ## Same_strand|Intronic_coding|ENSRNOT00000039603|ENSRNOG00000023908 ## ENSRNOG00000023908|protein_coding|NP_001101133.1|similar to MEGF6 (predicted) (RGD1307225_predicted), mRNA [Source:RefSeq_dna;Acc:NM_001107663] ## ENSRNOG00000036429|miRNA|rno-mir-551b|rno-mir-551b [Source:miRBase;Acc:MI0006343] ## {MIR: rno-mir-551b}
human	chromosome:3:169752320:169752446:1	Same_strand|Boundary_non-coding|ENST00000384984|ENSG00000207717|miRNA|hsa-mir-551b [Source:miRBase;Acc:MI0003575] ## {MIR: hsa-mir-551b}
mouse	chromosome:3:29315725:29315862:1	Same_strand|Boundary_non-coding|ENSMUST00000099169|ENSMUSG00000063600|protein_coding|RIKEN cDNA 6130401L20 gene Gene [Source:MGI Symbol;Acc:MGI:1922990] ## Same_strand|Intronic_coding|ENSMUST00000118531|ENSMUSG00000063600|protein_coding|RIKEN cDNA 6130401L20 gene Gene [Source:MGI Symbol;Acc:MGI:1922990] ## {MIR: mmu-mir-551b}

rno-mir-344

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-344 5arm	0.500	0	0	0	0	0	0	0	0	0
rno-mir-344 3arm	550.500	501	0	3	1.500	1	1	3.500	2	2.500
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-344 5arm	0.000	0	0	0	0	0	0	0	0	0
rno-mir-344 3arm	0.018	0.022	0	0.000	0.000	0.000	0.000	0.000	0.000	0.000

sblock654 (miRBase rno-mir-344-1) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-344-1

0.001

no

no

0.47/0.58

18/25/0.80

0.0 0.0

0.0 1.9

1 1066

0 0

1 9

0 0

22 15

4 6

5arm 3arm

2 2

nd nd

0.17 0.06

2 1

1299

9

2

4

Families

Member of family miR-344 (seed GAUCUAG): rno-mir-344, rno-mir-344

		reads	miRBase family seed
seed	-------------------------------------------------------------GAUCUAG------------------------------	1243	miR-344
seed	-----------------------------------------------------------CUGAUCU--------------------------------	37	novel
seed	--------------------------------------------------------------AUCUAGC-----------------------------	9	novel
seed	-----------------------------------------------------------------UAGCCAA--------------------------	5	novel
seed	----------------------------------------------------------CCUGAUC---------------------------------	2	novel
seed	------------------------------------------------------------UGAUCUA-------------------------------	2	novel
seed	-----------------------CAGGCUC--------------------------------------------------------------------	1	miR-344/484
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-344-3p	------------------------------------------------------------TGATCTAGCCAAAGCCTGACCGT---------------	23	219	229	2	1	-	-	2	-	2
	------------------------------------------------------------TGATCTAGCCAAAGCCTGACC-----------------	21	140	103	-	-	1	-	-	-	-
	------------------------------------------------------------TGATCTAGCCAAAGCCTG--------------------	18	91	101	1	-	-	1	-	1	-
	------------------------------------------------------------TGATCTAGCCAAAGCCTGAC------------------	20	102	81	-	1	-	1	-	2	-
	------------------------------------------------------------TGATCTAGCCAAAGCCTGACCG----------------	22	65	47	-	-	-	-	1	-	-
	------------------------------------------------------------TGATCTAGCCAAAGCCTGA-------------------	19	17	24	-	-	-	-	-	1	1
	----------------------------------------------------------CCTGATCTAGCCAAAGCCTGAC------------------	22	11	6	1	-	-	-	1	-	-
	----------------------------------------------------------CCTGATCTAGCCAAAGCC----------------------	18	9	3	-	-	-	-	-	-	-
	-------------------------------------------------------------GATCTAGCCAAAGCCTGACCGT---------------	22	3	3	-	-	-	-	-	-	-
	----------------------------------------------------------------CTAGCCAAAGCCTGACCGT---------------	19	1	4	-	-	-	-	-	-	-
	------------------------------------------------------------TGATCTAGCCAAAGCCTGACCGTA--------------	24	1	3	-	-	-	-	-	-	-
	----------------------------------------------------------CCTGATCTAGCCAAAGCCTG--------------------	20	2	1	-	-	-	-	-	-	-
	------------------------------------------------------------TGATCTAGCCAAAGCCTGACCGTAA-------------	25	1	1	-	-	-	-	-	-	-
	----------------------------------------------------------CCTGATCTAGCCAAAGCCT---------------------	19	2	-	-	-	-	-	-	-	-
	-----------------------------------------------------------CTGATCTAGCCAAAGCCTGACC-----------------	22	2	-	-	-	-	-	-	-	-
	-------------------------------------------------------------GATCTAGCCAAAGCCTGACC-----------------	20	1	1	-	-	-	-	-	-	-
	---------------------------------------------------------ACCTGATCTAGCCAAAGCCTGAC------------------	23	-	1	-	-	-	-	-	-	-
	----------------------------------------------------------CCTGATCTAGCCAAAGCCTGA-------------------	21	1	-	-	-	-	-	-	-	-
	----------------------TCAGGCTCCTGGCTAGATTC--------------------------------------------------------	20	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------ACCTGATCTAGCCAAAGCCT---------------------	20	-	1	-	-	-	-	-	-	-
	-------------------------------------------------------------GATCTAGCCAAAGCCTGACCG----------------	21	-	1	-	-	-	-	-	-	-
rno-miR-344-5p	----------------------TCAGGCTCCTGGCTAGATTCCAGG----------------------------------------------------	24	-	-	-	-	-	-	-	-	-
rat	CTGCAGCCAGAGTTTTTACCAGTCAGGCTCCTGGCTAGATTCCAGGTACCAACTGGTACCTGATCTAGCCAAAGCCTGACCGTAAGCTGCAAAAGAAA
mouse	-------------------CAGTCAGGCTCCTGGCTAGATTCCAGGTACCAACTGGTACCTGATCTAGCCAAAGCCTGACTG----------------
	************************************************************* *
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053682 ENSRNOG00000035559 rno-mir-344-1
rat	.((((((........((((..((((((((..(((((((((..((((((((....))))))))))))))))).)))))))).)))))))))).......	1.000 -52.10
mouse	((((((((((..(((((((((..((((((((....))))))))))))))))).))))))))))	1.000 -45.80

rat	chromosome:1:116020984:116021081:-1	Same_strand|Exonic_non-coding|ENSRNOT00000053682|ENSRNOG00000035559 ## ENSRNOG00000035559|miRNA|rno-mir-344-1|rno-mir-344-1 [Source:miRBase;Acc:MI0000629] ## {MIR: rno-mir-344-1}
mouse	chromosome:7:69084887:69085024:-1	Same_strand|Boundary_non-coding|ENSMUST00000083562|ENSMUSG00000065496|miRNA|mmu-mir-344-2 [Source:miRBase;Acc:MI0005495] ## {MIR: mmu-mir-344-2}

rno-mir-671

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-671 5arm	102	296	35	27	66	76	41	126	196	62
rno-mir-671 3arm	259	174	128	94	46	34	42	39	18	37
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-671 5arm	0.003	0.013	0.002	0.002	0.003	0.006	0.003	0.007	0.013	0.004
rno-mir-671 3arm	0.009	0.008	0.007	0.006	0.002	0.003	0.003	0.002	0.001	0.002

sblock8332 (miRBase rno-mir-671) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-671

0.001

no

no

0.63/0.72

18/25/0.75

0.0 0.0

0.9 1.0

571 437

0 0

10 10

0 0

10 9

5 7

5arm 3arm

1 1

nd nd

0.13 0.04

2 1

1898

10

1

4

		reads	miRBase family seed
seed	-----------------------------GGAAGCC----------------------------------------------------------------------------------	1027	novel
seed	--------------------------------------------------------------------CCGGUUC-------------------------------------------	844	miR-671
seed	-------------------------------------------------------------------UCCGGUU--------------------------------------------	21	novel
seed	-----------------------------------------------------------------CCUCCGG----------------------------------------------	3	novel
seed	---------------------------------------------------------------------CGGUUCU------------------------------------------	2	novel
seed	----------------------------------------------------------------------GGUUCUC-----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------AGGAAGCCCTGGAGGGGCTGG---------------------------------------------------------------------	21	33	95	11	7	18	34	14	44	39	18
rno-miR-671	-------------------------------------------------------------------TCCGGTTCTCAGGGCTCCACC------------------------------	21	85	69	26	19	12	11	16	15	7	12
	-------------------------------------------------------------------TCCGGTTCTCAGGGCTCCAC-------------------------------	20	59	34	26	32	10	4	10	9	6	13
	----------------------------AGGAAGCCCTGGAGGGGCTG----------------------------------------------------------------------	20	13	47	6	4	19	15	5	29	48	15
	----------------------------AGGAAGCCCTGGAGGGGCT-----------------------------------------------------------------------	19	30	32	11	5	7	11	11	21	43	10
	----------------------------AGGAAGCCCTGGAGGGGCTGGAG-------------------------------------------------------------------	23	10	62	5	5	11	5	3	12	35	9
	-------------------------------------------------------------------TCCGGTTCTCAGGGCTCCACCTC----------------------------	23	47	25	10	16	-	9	6	6	2	7
	-------------------------------------------------------------------TCCGGTTCTCAGGGCTCC---------------------------------	18	26	16	33	9	7	4	3	5	2	2
	----------------------------AGGAAGCCCTGGAGGGGC------------------------------------------------------------------------	18	10	24	-	4	9	7	7	7	12	6
	-------------------------------------------------------------------TCCGGTTCTCAGGGCTCCA--------------------------------	19	23	19	14	9	9	4	3	2	-	2
	----------------------------AGGAAGCCCTGGAGGGGCTGGA--------------------------------------------------------------------	22	3	21	1	1	1	4	1	5	12	-
	-------------------------------------------------------------------TCCGGTTCTCAGGGCTCCACCT-----------------------------	22	14	7	12	6	7	-	2	1	-	-
	----------------------------AGGAAGCCCTGGAGGGGCTGGAGG------------------------------------------------------------------	24	2	14	1	1	1	-	-	2	5	4
	------------------------------------------------------------------CTCCGGTTCTCAGGGCTCCAC-------------------------------	21	2	-	5	1	-	-	1	-	1	1
	----------------------------AGGAAGCCCTGGAGGGGCTGGAGGT-----------------------------------------------------------------	25	1	1	-	-	-	-	-	6	2	-
	------------------------------------------------------------------CTCCGGTTCTCAGGGCTCCACC------------------------------	22	2	1	-	-	1	-	1	-	-	-
	------------------------------------------------------------------CTCCGGTTCTCAGGGCTCCA--------------------------------	20	-	-	1	1	-	1	-	-	-	-
	----------------------------------------------------------------TCCTCCGGTTCTCAGGGC------------------------------------	18	-	-	1	-	-	1	-	-	-	-
	--------------------------------------------------------------------CCGGTTCTCAGGGCTCCACC------------------------------	20	-	2	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------CGGTTCTCAGGGCTCCACC------------------------------	19	-	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------------TCCTCCGGTTCTCAGGGCTCCA--------------------------------	22	1	-	-	-	-	-	-	-	-	-
	------------------------------------------------------------------CTCCGGTTCTCAGGGCTCCACCTC----------------------------	24	-	-	-	1	-	-	-	-	-	-
	------------------------------------------------------------------CTCCGGTTCTCAGGGCTCC---------------------------------	19	-	-	-	-	-	-	-	1	-	-
rat	------------------CAGGAAGAGGAGGAAGCCCTGGAGGGGCTGGAGGTGATGGATGTTTTCCTCCGGTTCTCAGGGCTCCACCTCTTTCGAGCC-------------------
human	GCAGGTGAACTGGCAGGCCAGGAAGAGGAGGAAGCCCTGGAGGGGCTGGAGGTGATGGATGTTTTCCTCCGGTTCTCAGGGCTCCACCTCTTTCGGGCCGTAGAGCCAGGGCTGGTGC
mouse	GCTGGCGAACTGGCAGGCCAGGAAGAGGAGGAAGCCCTGGAGGGGCTGGAGGTGATGGATGTTTTCCTCCGGTTCTCAGGGCTCCACCTCTTTCGAGCCGTAGAGCCAGGGCTGGT--
	***************************************************************************** ***
	>>>>>                  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                   >>>>>	ENSRNOT00000014082 ENSRNOG00000010466 NP_001100044.1
	>>>>>                  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                   >>>>>	ENSRNOT00000036919 ENSRNOG00000010466 NP_001100044.1
	>>>>>                  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                   >>>>>	ENSRNOT00000062099 ENSRNOG00000040346 rno-mir-671
rat	..((((((((.(((.((((((..(((((((((((.(((....)))..)))))))))))))))))))).)))))))).....	1.000 -47.00
human	((((((...(((((.((((.((((((((.((.(((((((..((..(((((((.(((....)))..)))))))..))))))))))).)))))))).)))).....))))).)))..)))	0.983 -66.70
mouse	((..((...(((((.(((..((((((((.((.(((((((..((..(((((((.(((....)))..)))))))..))))))))))).))))))))..))).....))))).))..))	1.000 -67.60

rat	chromosome:4:5960209:5960289:-1	Same_strand|Exonic_non-coding|ENSRNOT00000062099|ENSRNOG00000040346 ## Same_strand|Exonic_coding|ENSRNOT00000036919|ENSRNOG00000010466 ## ENSRNOG00000040346|miRNA|rno-mir-671|rno-mir-671 [Source:miRBase;Acc:MI0006156] ## ENSRNOG00000010466|protein_coding|NP_001100044.1|similar to mKIAA1402 protein (predicted) (RGD1306404_predicted), mRNA [Source:RefSeq_dna;Acc:NM_001106574] ## {MIR: rno-mir-671}
human	chromosome:7:150566440:150566557:1	Same_strand|Intronic_coding|ENST00000377851|ENSG00000033100|protein_coding|Chondroitin sulfate glucuronyltransferase (EC 2.4.1.226)(N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase)(Chondroitin glucuronyltransferase II)(CSGlcA-T) [Source:UniProtKB/Swiss-Prot;Acc:Q9P2E5] ## Same_strand|Exonic_coding|ENST00000035307|ENSG00000033100|protein_coding|Chondroitin sulfate glucuronyltransferase (EC 2.4.1.226)(N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase)(Chondroitin glucuronyltransferase II)(CSGlcA-T) [Source:UniProtKB/Swiss-Prot;Acc:Q9P2E5] ## Same_strand|Exonic_non-coding|ENST00000390183|ENSG00000211517|miRNA|hsa-mir-671 [Source:miRBase;Acc:MI0003760] ## {MIR: hsa-mir-671}
mouse	chromosome:5:24097922:24098037:1	Same_strand|Exonic_coding|ENSMUST00000121863|ENSMUSG00000038181|protein_coding|RIKEN cDNA 2010209O12 gene Gene [Source:MGI Symbol;Acc:MGI:1917522] ## Same_strand|Boundary_non-coding|ENSMUST00000102432|ENSMUSG00000076387|miRNA|mmu-mir-671 [Source:miRBase;Acc:MI0004133] ## {MIR: mmu-mir-671}

rno-mir-489

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-489 5arm	6	3	0	0	0	0	0	0	19	39
rno-mir-489 3arm	148	65	2	0	0	1	1	0	180	263
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-489 5arm	0.000	0.000	0	0	0	0	0	0	0.001	0.003
rno-mir-489 3arm	0.005	0.003	0.000	0	0	0.000	0.000	0	0.012	0.017

sblock8358 (miRBase rno-mir-489) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-489

0.001

no

no

0.28/0.52

18/26/0.81

0.0 0.0

0.0 0.7

30 453

0 0

4 7

0 0

22 24

7 5

5arm 3arm

1 1

nd nd

0.20 0.09

3 1

727

7

-2

2

Clusters

Located in cluster 49: hsa-mir-653, rno-mir-489

		reads	miRBase family seed
seed	-------------------------------------------------------------UGACAUC--------------------------------------	536	novel
seed	------------------------------------------------------------AUGACAU---------------------------------------	97	miR-489
seed	-----------------------GUCGUAU----------------------------------------------------------------------------	67	novel
seed	--------------------------------------------------------------GACAUCA-------------------------------------	25	novel
seed	---------------------------------------------------------------ACAUCAC------------------------------------	1	novel
seed	----------------------------------------------------------------CAUCACA-----------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2	T4S1	T5S1	T5S2
	------------------------------------------------------------ATGACATCACATATATGGCAG-------------------------	21	56	13	1	-	-	62	80
	------------------------------------------------------------ATGACATCACATATATGGCA--------------------------	20	26	27	1	1	-	34	64
	------------------------------------------------------------ATGACATCACATATATGGCAGC------------------------	22	39	8	-	-	-	23	41
	------------------------------------------------------------ATGACATCACATATATGG----------------------------	18	8	6	-	-	-	11	24
	-----------------------------------------------------------AATGACATCACATATATG-----------------------------	18	5	4	-	-	1	22	16
	----------------------TGTCGTATGCGTGATGACAC----------------------------------------------------------------	20	5	1	-	-	-	10	20
	-----------------------------------------------------------AATGACATCACATATATGGCA--------------------------	21	1	4	-	-	-	4	6
	-----------------------------------------------------------AATGACATCACATATATGGCAG-------------------------	22	1	-	-	-	-	6	6
	-----------------------------------------------------------AATGACATCACATATATGG----------------------------	19	2	-	-	-	-	1	7
rno-miR-489	-----------------------------------------------------------AATGACATCACATATATGGCAGC------------------------	23	1	-	-	-	-	6	2
	-------------------------------------------------------------TGACATCACATATATGGCAGC------------------------	21	2	1	-	-	-	3	3
	------------------------------------------------------------ATGACATCACATATATGGC---------------------------	19	5	-	-	-	-	1	2
	----------------------TGTCGTATGCGTGATGACACGT--------------------------------------------------------------	22	1	-	-	-	-	2	5
	----------------------TGTCGTATGCGTGATGAC------------------------------------------------------------------	18	-	1	-	-	-	1	5
	-------------------------------------------------------------TGACATCACATATATGGCA--------------------------	19	-	1	-	-	-	4	1
	-------------------------------------------------------------TGACATCACATATATGGCAG-------------------------	20	1	-	-	-	-	2	3
	----------------------TGTCGTATGCGTGATGACA-----------------------------------------------------------------	19	-	1	-	-	-	2	2
	----------------------TGTCGTATGCGTGATGACACG---------------------------------------------------------------	21	-	-	-	-	-	2	3
	----------------------TGTCGTATGCGTGATGACACGTTC------------------------------------------------------------	24	-	-	-	-	-	1	3
	-------------------------------------------------------------TGACATCACATATATGGCAGCT-----------------------	22	-	1	-	-	-	-	2
	------------------------------------------------------------ATGACATCACATATATGGCAGCT-----------------------	23	-	-	-	-	-	-	3
	----------------------TGTCGTATGCGTGATGACACGTTCTC----------------------------------------------------------	26	-	-	-	-	-	1	1
	-----------------------------------------------------------AATGACATCACATATATGGC---------------------------	20	-	-	-	-	-	-	2
	---------------------------------------------------------------ACATCACATATATGGCAGC------------------------	19	-	-	-	-	-	1	-
	-------------------------------------------------------------TGACATCACATATATGGC---------------------------	18	1	-	-	-	-	-	-
	--------------------------------------------------------------GACATCACATATATGGCA--------------------------	18	-	-	-	-	-	-	1
rat	ACTGCTACAGTGGCAGCTTGGTTGTCGTATGCGTGATGACACGTTCTCGTGTATTCCAGAATGACATCACATATATGGCAGCTAAACTGTTACAGGAACAACAAGT
human	--------------------GTGGTCGTATGTGTGACGCCATTTACTTGAACCTTTAGGAGTGACATCACATATACGGCAGC------------------------
	** ******** **** * **  * ** *    **   ** ************** ******
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000013910 ENSRNOG00000010053 Calcr
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000013937 ENSRNOG00000010053 Calcr
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000054394 ENSRNOG00000036271 rno-mir-489
rat	.........(((((((.((((((((((((((.((((((...((((((.(......).)))))).)))))).)))))))))))))).))))))).............	1.000 -39.90
human	...(((((((((((((...((((..(((((....)))))))))...)))))))))))))...	0.972 -21.70

rat	chromosome:4:28518260:28518365:-1	Same_strand|Intronic_coding|ENSRNOT00000013937|ENSRNOG00000010053 ## Same_strand|Exonic_non-coding|ENSRNOT00000054394|ENSRNOG00000036271 ## ENSRNOG00000036271|miRNA|rno-mir-489|rno-mir-489 [Source:miRBase;Acc:MI0003477] ## ENSRNOG00000010053|protein_coding|Calcr|Calcitonin receptor precursor (CT-R) (C1A/C1B). [Source:UniProtKB/Swiss-Prot;Acc:P32214] ## {MIR: rno-mir-489}
human	chromosome:7:92951151:92951296:-1	Same_strand|Intronic_coding|ENST00000359558|ENSG00000004948|protein_coding|Calcitonin receptor Precursor (CT-R) [Source:UniProtKB/Swiss-Prot;Acc:P30988] ## Same_strand|Boundary_non-coding|ENST00000384923|ENSG00000207656|miRNA|hsa-mir-489 [Source:miRBase;Acc:MI0003124] ## {MIR: hsa-mir-489}

rno-mir-32

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-32 5arm	26	25	41	35	115	101	10	32	73	108
rno-mir-32 3arm	11	4	4	2	4	13	0	1	6	18
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-32 5arm	0.001	0.001	0.002	0.002	0.006	0.008	0.001	0.002	0.005	0.007
rno-mir-32 3arm	0.000	0.000	0.000	0.000	0.000	0.001	0	0.000	0.000	0.001

sblock9334 (miRBase rno-mir-32) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-32

0.001

no

no

0.25/0.39

18/23/0.77

0.0 0.2

0.0 1.1

284 41

0 0

10 9

0 0

5 2

8 7

5arm 3arm

1 1

nd nd

0.15 0.09

2 2

629

10

-2

3

Families

Member of family miR-25/32/363/92a/92b (seed AUUGCAC): rno-mir-25, rno-mir-363, rno-mir-92a, rno-mir-92b, rno-mir-32, rno-mir-92a

		reads	miRBase family seed
seed	-------------------------AUUGCAC-----------------------------------------------------------------------------	538	miR-25/32/363/92a/92b
seed	------------------------------------------------------------------AAUUUAG------------------------------------	40	novel
seed	-----------------------------------------------------------------CAAUUUA-------------------------------------	15	novel
seed	--------------------------UUGCACA----------------------------------------------------------------------------	15	novel
seed	------------------------UAUUGCA------------------------------------------------------------------------------	11	novel
seed	----------------------------------------------------------------GCAAUUU--------------------------------------	6	novel
seed	----------------------------GCACAUU--------------------------------------------------------------------------	2	novel
seed	---------------------------------------------------------------UGCAAUU---------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------TATTGCACATTACTAAGTTG-----------------------------------------------------------------	20	21	13	24	16	69	56	6	19	44	70
	------------------------TATTGCACATTACTAAGTTGC----------------------------------------------------------------	21	2	3	1	6	14	17	1	4	9	14
	------------------------TATTGCACATTACTAAGT-------------------------------------------------------------------	18	1	-	8	7	12	11	2	5	7	10
	------------------------TATTGCACATTACTAAGTT------------------------------------------------------------------	19	1	3	3	-	6	9	1	3	3	5
rno-miR-32	------------------------TATTGCACATTACTAAGTTGCA---------------------------------------------------------------	22	1	4	2	3	8	4	-	1	4	4
	-----------------------------------------------------------------CAATTTAGTGTGTGTGATA-------------------------	19	3	2	-	1	3	6	-	-	-	4
	-----------------------------------------------------------------CAATTTAGTGTGTGTGATATTC----------------------	22	2	-	-	-	-	1	-	-	4	5
	-------------------------ATTGCACATTACTAAGTTG-----------------------------------------------------------------	19	-	-	2	-	4	-	-	-	-	1
	----------------------------------------------------------------GCAATTTAGTGTGTGTGA---------------------------	18	-	-	1	-	-	1	-	-	-	4
	-----------------------------------------------------------------CAATTTAGTGTGTGTGAT--------------------------	18	1	-	2	-	-	2	-	-	-	1
	-------------------------ATTGCACATTACTAAGTTGC----------------------------------------------------------------	20	-	-	1	-	-	-	-	-	3	1
	-----------------------ATATTGCACATTACTAAGT-------------------------------------------------------------------	19	-	-	-	-	1	2	-	-	1	-
	----------------------------------------------------------------GCAATTTAGTGTGTGTGATA-------------------------	20	1	-	-	-	-	1	-	-	-	2
	---------------------------------------------------------------TGCAATTTAGTGTGTGTGA---------------------------	19	1	-	-	-	1	1	-	-	-	-
	----------------------------------------------------------------GCAATTTAGTGTGTGTGATATTC----------------------	23	-	1	-	-	-	-	-	-	1	1
	-----------------------------------------------------------------CAATTTAGTGTGTGTGATAT------------------------	20	1	-	-	-	-	1	-	-	-	1
	---------------------------------------------------------------TGCAATTTAGTGTGTGTGAT--------------------------	20	2	-	-	-	-	-	-	1	-	-
	-----------------------ATATTGCACATTACTAAGTTGC----------------------------------------------------------------	22	-	-	-	-	1	-	-	-	1	1
	-----------------------ATATTGCACATTACTAAGTTG-----------------------------------------------------------------	21	-	-	-	-	-	1	-	-	-	1
	-------------------------ATTGCACATTACTAAGTT------------------------------------------------------------------	18	-	-	-	2	-	-	-	-	-	-
	---------------------------TGCACATTACTAAGTTGC----------------------------------------------------------------	18	-	-	-	-	-	-	-	-	1	1
	----------------------------------------------------------------GCAATTTAGTGTGTGTGATAT------------------------	21	-	-	1	-	-	-	-	-	-	-
	-------------------------ATTGCACATTACTAAGTTGCA---------------------------------------------------------------	21	-	-	-	-	-	1	-	-	-	-
	-----------------------ATATTGCACATTACTAAGTT------------------------------------------------------------------	20	-	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------ATGCAATTTAGTGTGTGTGA---------------------------	20	-	-	-	-	-	-	-	-	1	-
	----------------------------------------------------------------GCAATTTAGTGTGTGTGAT--------------------------	19	-	-	-	1	-	-	-	-	-	-
	------------------------TATTGCACATTACTAAGTTGCAT--------------------------------------------------------------	23	-	-	-	1	-	-	-	-	-	-
	-----------------------ATATTGCACATTACTAAG--------------------------------------------------------------------	18	-	1	-	-	-	-	-	-	-	-
	--------------------------------------------------------------ATGCAATTTAGTGTGTGTGAT--------------------------	21	-	1	-	-	-	-	-	-	-	-
rat	-------------------GGGGATATTGCACATTACTAAGTTGCATGTTGTCACGGCCTCAATGCAATTTAGTGTGTGTGATATTCTC--------------------
human	CCATTCTGCTTGCTCTGGTGGAGATATTGCACATTACTAAGTTGCATGTTGTCACGGCCTCAATGCAATTTAGTGTGTGTGATATTTTCACATGAGTGCATGCACACGG
mouse	CC-CTCTGCTTGCTCTGGTGGAGATATTGCACATTACTAAGTTGCATGTTGTCACGGCCTCAATGCAATTTAGTGTGTGTGATATTTTCACATGAGTGCATGCACACGG
	** **************************************************************** **
	.....                   >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                    .....	ENSRNOT00000053635 ENSRNOG00000035512 rno-mir-32
rat	((((((((..(((((.(((((((((((((..((....))..).)))))))))))))))))..))))))))	1.000 -33.60
human	......(((.(((.((.((((((((((..((((.((((((((((((((..((....))..)).))))))))))))))))..))))))))))...)).))).))).....	0.999 -46.30
mouse	(( ...(((.(((.((.((((((((((..((((.((((((((((((((..((....))..)).))))))))))))))))..))))))))))...)).))).)))...))	1.000 -46.80

rat	chromosome:5:74797826:74797895:-1	Same_strand|Exonic_non-coding|ENSRNOT00000053635|ENSRNOG00000035512 ## ENSRNOG00000035512|miRNA|rno-mir-32|rno-mir-32 [Source:miRBase;Acc:MI0000873] ## {MIR: rno-mir-32}
human	chromosome:9:110848310:110848418:-1	Same_strand|Intronic_coding|ENST00000374586|ENSG00000106771|protein_coding|Transmembrane protein C9orf5 (Protein CG-2) [Source:UniProtKB/Swiss-Prot;Acc:Q9H330] ## Same_strand|Boundary_non-coding|ENST00000384965|ENSG00000207698|miRNA|hsa-mir-32 [Source:miRBase;Acc:MI0000090] ## {MIR: hsa-mir-32}
mouse	chromosome:4:56908081:56908188:-1	Same_strand|Intronic_coding|ENSMUST00000068792|ENSMUSG00000055296|protein_coding|Likely ortholog of H. sapiens chromosome 9 open reading frame 5 (C9orf5) [Source:UniProtKB/TrEMBL;Acc:B1AZA5] ## Same_strand|Boundary_non-coding|ENSMUST00000083610|ENSMUSG00000065544|miRNA|mmu-mir-32 [Source:miRBase;Acc:MI0000691] ## {MIR: mmu-mir-32}

rno-mir-101a

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-101a 5arm	120.500	59.500	12.500	14	39	31	14.500	38	55.500	68.500
rno-mir-101a 3arm	6421.500	3907	1060.500	1614	2057	1813	1593.500	2238	3980.500	5228.500
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-101a 5arm	0.004	0.003	0.001	0.001	0.002	0.002	0.001	0.002	0.004	0.005
rno-mir-101a 3arm	0.213	0.171	0.057	0.096	0.100	0.137	0.124	0.118	0.262	0.348

sblock9477 (miRBase rno-mir-101a) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-101a

0.001

no

no

0.33/0.48

18/26/0.71

0.1 0.0 0.5 0.0

0.0 0.0 2.2 0.8

185 1 4 16236

0 0 0 0

10 1 3 10

0 0 0 0

9 20 16 8

1 -9 -18 1

5arm_loop 5arm_loop 3arm_loop 3arm

1 1 1 2

nd nd nd nd

0.05 0.52 0.38 0.00

1 10 10 0

35927

10

0

1

Families

Member of family miR-101a/101b (seed ACAGUAC): rno-mir-101b, rno-mir-101a, rno-mir-101a

		reads	miRBase family seed
seed	------------------------------------------------------------------UACAGUA----------------------------------------	28768	novel
seed	-------------------------------------------------------------------ACAGUAC---------------------------------------	6344	miR-101a/101b
seed	------------------------------CAGUUAU----------------------------------------------------------------------------	346	miR-101a*
seed	--------------------------------------------------------------------CAGUACU--------------------------------------	261	novel
seed	-------------------------------AGUUAUC---------------------------------------------------------------------------	151	novel
seed	---------------------------------------------------------------------AGUACUG-------------------------------------	41	novel
seed	-----------------------------------------------------------------GUACAGU-----------------------------------------	11	novel
seed	----------------------------------------------------GUCCAUU------------------------------------------------------	3	novel
seed	-----------------------------------------GUGCUGA-----------------------------------------------------------------	1	novel
seed	------------------------------------------------------CCAUUCU----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------------------------------------GTACAGTACTGTGATAACTGA---------------------------	21	2995	1930	415	656	897	839	645	941	2101	2252
	-----------------------------------------------------------------GTACAGTACTGTGATAAC------------------------------	18	1616	909	246	367	482	471	337	422	694	1024
	-----------------------------------------------------------------GTACAGTACTGTGATAACTGAA--------------------------	22	1178	822	141	208	319	244	188	332	667	1290
	------------------------------------------------------------------TACAGTACTGTGATAACTGA---------------------------	20	447	206	135	199	216	167	247	267	268	377
	-----------------------------------------------------------------GTACAGTACTGTGATAACT-----------------------------	19	440	313	86	140	181	171	118	135	269	256
rno-miR-101a	------------------------------------------------------------------TACAGTACTGTGATAACTGAA--------------------------	21	381	152	105	162	133	126	147	210	248	365
	-----------------------------------------------------------------GTACAGTACTGTGATAACTG----------------------------	20	231	120	22	46	57	51	33	88	98	192
	------------------------------------------------------------------TACAGTACTGTGATAACT-----------------------------	18	159	64	50	80	85	69	88	77	71	84
	------------------------------------------------------------------TACAGTACTGTGATAACTG----------------------------	19	118	27	30	57	38	50	37	50	60	91
	------------------------------------------------------------------TACAGTACTGTGATAACTGAAG-------------------------	22	66	37	16	21	39	12	19	45	43	58
rno-miR-101a*	-----------------------------TCAGTTATCACAGTGCTGATGC--------------------------------------------------------------	22	59	26	5	6	19	18	1	12	24	19
	-------------------------------------------------------------------ACAGTACTGTGATAACTGA---------------------------	19	15	14	19	5	8	4	15	18	17	8
	-------------------------------------------------------------------ACAGTACTGTGATAACTGAA--------------------------	20	13	6	6	14	3	6	7	19	8	17
	-----------------------------------------------------------------GTACAGTACTGTGATAACTGAAG-------------------------	23	15	9	2	1	13	2	11	8	18	10
	------------------------------CAGTTATCACAGTGCTGATGC--------------------------------------------------------------	21	20	10	1	2	7	2	-	5	6	11
	-----------------------------TCAGTTATCACAGTGCTGA-----------------------------------------------------------------	19	4	5	3	2	4	4	7	10	3	9
	-----------------------------TCAGTTATCACAGTGCTGATGCT-------------------------------------------------------------	23	8	5	3	-	2	2	1	5	6	13
	------------------------------------------------------------------TACAGTACTGTGATAACTGAAGG------------------------	23	12	3	1	1	1	2	1	4	3	6
	-----------------------------TCAGTTATCACAGTGCTGAT----------------------------------------------------------------	20	7	3	1	2	-	2	3	6	-	9
	------------------------------CAGTTATCACAGTGCTGA-----------------------------------------------------------------	18	11	1	-	-	2	2	2	1	4	4
	------------------------------CAGTTATCACAGTGCTGATG---------------------------------------------------------------	20	6	3	-	1	3	1	3	3	4	2
	-------------------------------------------------------------------ACAGTACTGTGATAACTG----------------------------	18	5	3	1	2	1	-	4	2	3	4
	-----------------------------TCAGTTATCACAGTGCTG------------------------------------------------------------------	18	2	5	2	-	2	-	-	1	4	2
	------------------------------CAGTTATCACAGTGCTGATGCT-------------------------------------------------------------	22	1	3	-	1	1	1	-	-	5	5
	------------------------------CAGTTATCACAGTGCTGAT----------------------------------------------------------------	19	7	2	-	-	2	-	2	-	2	1
	--------------------------------------------------------------------CAGTACTGTGATAACTGAA--------------------------	19	4	-	-	1	1	2	2	3	1	2
	-------------------------------------------------------------------ACAGTACTGTGATAACTGAAG-------------------------	21	2	1	-	-	-	-	1	1	4	5
	--------------------------------------------------------------------CAGTACTGTGATAACTGAAG-------------------------	20	1	2	2	-	1	1	-	1	1	4
	------------------------------------------------------------------TACAGTACTGTGATAACTGAAGGA-----------------------	24	-	1	1	-	3	1	-	-	2	3
	--------------------------------------------------------------------CAGTACTGTGATAACTGA---------------------------	18	1	2	-	-	-	1	2	2	-	3
	-----------------------------TCAGTTATCACAGTGCTGATG---------------------------------------------------------------	21	1	2	-	1	1	1	-	1	3	-
	----------------------------------------------------------------GGTACAGTACTGTGATAACTGA---------------------------	22	4	1	-	-	1	-	-	-	-	1
	---------------------------------------------------TGTCCATTCTAAAGGTACA-------------------------------------------	19	2	-	-	-	-	1	-	-	-	-
	----------------------------------------------------------------GGTACAGTACTGTGATAACTG----------------------------	21	2	-	-	-	-	-	-	-	1	-
	-----------------------------------------------------------------GTACAGTACTGTGATAACTGAAGG------------------------	24	1	2	-	-	-	-	-	-	-	-
	------------------------------CAGTTATCACAGTGCTGATGCTGT-----------------------------------------------------------	24	-	-	-	-	-	-	-	-	-	1
	----------------------------------------------------------------GGTACAGTACTGTGATAAC------------------------------	19	-	-	-	-	-	-	-	-	-	1
	-----------------------------------------------------TCCATTCTAAAGGTACAGTACTGTGA----------------------------------	26	-	1	-	-	-	-	-	-	-	-
	----------------------------------------AGTGCTGATGCTGTCCATTCT----------------------------------------------------	21	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------GTACAGTACTGTGATAACTGAAGGA-----------------------	25	-	-	-	-	-	-	-	-	1	-
	--------------------------------------------------------------------CAGTACTGTGATAACTGAAGG------------------------	21	-	-	-	-	-	-	-	-	-	1
rat	--------------------TGCCCTGGCTCAGTTATCACAGTGCTGATGCTGTCCATTCTAAAGGTACAGTACTGTGATAACTGAAGGATGGCA------------------
human	-----------------GGCTGCCCTGGCTCAGTTATCACAGTGCTGATGCTGTCTATTCTAAAGGTACAGTACTGTGATAACTGAAGGATGGCAGCCATCTTACCTTCCATC
mouse	GGACACGGTGACTGACAGGCTGCCCTGGCTCAGTTATCACAGTGCTGATGCTGTCCATTCTAAAGGTACAGTACTGTGATAACTGAAGGATGGCAGCCATCTTGCCTTCC---
	*********************************** ***************************************
	.>>>>                    >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                  >>>>.	ENSRNOT00000053722 ENSRNOG00000035599 rno-mir-101a
rat	.(((.....((((((((((((((((((.((((............)))))))))))))))))))))).....))).	1.000 -36.20
human	(((((((.....((((((((((((((((((.((((............)))))))))))))))))))))).....)))))))...............	1.000 -47.10
mouse	(((...(((((..((..(((((((.....((((((((((((((((((.((((............)))))))))))))))))))))).....))))))).))))))).)))	0.975 -50.70

rat	chromosome:5:121990585:121990659:-1	Same_strand|Exonic_non-coding|ENSRNOT00000053722|ENSRNOG00000035599 ## ENSRNOG00000035599|miRNA|rno-mir-101a|rno-mir-101a [Source:miRBase;Acc:MI0000886] ## {MIR: rno-mir-101a}
human	chromosome:1:65296687:65296782:-1	Same_strand|Boundary_non-coding|ENST00000362265|ENSG00000199135|miRNA|hsa-mir-101-1 [Source:miRBase;Acc:MI0000103] ## {MIR: hsa-mir-101-1}
mouse	chromosome:4:101019539:101019648:-1	Same_strand|Boundary_non-coding|ENSMUST00000083517|ENSMUSG00000065451|miRNA|mmu-mir-101a [Source:miRBase;Acc:MI0000148] ## {MIR: mmu-mir-101a}

rno-mir-200a

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-200a 5arm	27	0	11	6	3	2	1	0	115	193
rno-mir-200a 3arm	2841	54	301	341	170	304	38	74	4986	21333
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-200a 5arm	0.001	0	0.001	0.000	0.000	0.000	0.000	0	0.008	0.013
rno-mir-200a 3arm	0.094	0.002	0.016	0.020	0.008	0.023	0.003	0.004	0.329	1.419

sblock9643 (miRBase rno-mir-200a) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-200a

0.002

no

no

0.39/0.58

18/24/0.79

0.0 0.0

0.5 0.0

238 10779

0 0

8 10

0 0

15 14

6 5

5arm 3arm

1 1

nd nd

0.05 0.09

1 1

30800

10

0

1

Clusters

Located in cluster 61: rno-mir-429, rno-mir-200a, rno-mir-200b

Families

Member of family miR-141/200a (seed AACACUG): rno-mir-200a, rno-mir-141, rno-mir-141

		reads	miRBase family seed
seed	------------------------------------------------------AACACUG----------------------------	29023	miR-141/200a
seed	-------------------------------------------------------ACACUGU---------------------------	1241	novel
seed	----------------AUCUUAC------------------------------------------------------------------	354	novel
seed	--------------------------------------------------------CACUGUC--------------------------	107	novel
seed	----------------------------------------------------------CUGUCUG------------------------	48	novel
seed	---------------------------------------------------------ACUGUCU-------------------------	15	novel
seed	-----------------------------------------------------UAACACU-----------------------------	6	novel
seed	-----------------UCUUACC-----------------------------------------------------------------	3	novel
seed	-----------------------------------------------------------UGUCUGG-----------------------	2	novel
seed	---------------CAUCUUA-------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-miR-200a	-----------------------------------------------------TAACACTGTCTGGTAACGATGT--------------	22	1353	8	94	99	50	111	5	10	1453	10779
	-----------------------------------------------------TAACACTGTCTGGTAACGATG---------------	21	384	3	34	54	22	43	1	4	946	2858
	-----------------------------------------------------TAACACTGTCTGGTAACGA-----------------	19	359	3	48	43	18	35	3	2	846	2734
	-----------------------------------------------------TAACACTGTCTGGTAACGATGTTC------------	24	282	2	24	16	4	14	1	-	195	2291
	-----------------------------------------------------TAACACTGTCTGGTAACG------------------	18	160	1	18	25	3	15	1	-	516	1017
	-----------------------------------------------------TAACACTGTCTGGTAACGATGTT-------------	23	66	-	18	24	3	5	-	-	573	339
	-----------------------------------------------------TAACACTGTCTGGTAACGAT----------------	20	99	1	7	10	4	9	-	2	221	655
	------------------------------------------------------AACACTGTCTGGTAACGATGT--------------	21	57	9	14	18	17	20	9	11	99	347
	---------------CATCTTACCGGACAGTGC--------------------------------------------------------	18	13	-	4	5	2	1	1	-	67	96
	------------------------------------------------------AACACTGTCTGGTAACGAT----------------	19	12	4	9	9	14	14	1	11	32	71
	------------------------------------------------------AACACTGTCTGGTAACGA-----------------	18	17	10	5	7	7	15	6	9	40	60
	------------------------------------------------------AACACTGTCTGGTAACGATG---------------	20	17	5	9	4	6	5	-	2	36	85
	-------------------------------------------------------ACACTGTCTGGTAACGATGT--------------	20	13	5	6	20	14	10	2	5	2	10
	------------------------------------------------------AACACTGTCTGGTAACGATGTTC------------	23	9	-	1	3	-	-	-	1	4	65
	---------------CATCTTACCGGACAGTGCT-------------------------------------------------------	19	7	-	3	-	-	-	-	-	28	40
	---------------CATCTTACCGGACAGTGCTG------------------------------------------------------	20	5	-	2	-	-	-	-	-	9	35
	---------------------------------------------------------ACTGTCTGGTAACGATGT--------------	18	8	1	6	3	4	5	6	7	1	5
	------------------------------------------------------AACACTGTCTGGTAACGATGTT-------------	22	1	1	3	-	-	-	-	2	19	9
	---------------CATCTTACCGGACAGTGCTGG-----------------------------------------------------	21	1	-	1	1	1	-	-	-	5	15
	-------------------------------------------------------ACACTGTCTGGTAACGATG---------------	19	-	1	2	5	2	1	1	1	-	2
	--------------------------------------------------------CACTGTCTGGTAACGATGT--------------	19	3	-	2	-	1	2	1	5	-	-
	---------------CATCTTACCGGACAGTGCTGGA----------------------------------------------------	22	-	-	1	-	-	-	-	-	6	5
	-------------------------------------------------------ACACTGTCTGGTAACGAT----------------	18	1	-	-	-	-	-	-	2	-	1
	----------------------------------------------------CTAACACTGTCTGGTAACGATGT--------------	23	-	-	-	-	-	-	-	-	-	3
	----------------------------------------------------CTAACACTGTCTGGTAAC-------------------	18	-	-	-	-	-	-	-	-	2	-
	---------------------------------------------------------ACTGTCTGGTAACGATGTT-------------	19	-	-	1	-	-	-	1	-	-	-
	----------------------------------------------------CTAACACTGTCTGGTAACGATG---------------	22	-	-	-	-	-	-	-	-	-	1
	--------------------------------------------------------CACTGTCTGGTAACGATG---------------	18	-	-	-	-	1	-	-	-	-	-
	----------------------------------------------------------CTGTCTGGTAACGATGTT-------------	18	-	-	-	1	-	-	-	-	-	-
	----------------ATCTTACCGGACAGTGCTGG-----------------------------------------------------	20	1	-	-	-	-	-	-	-	-	-
	--------------GCATCTTACCGGACAGTGC--------------------------------------------------------	19	-	-	-	-	-	-	-	-	-	1
	----------------ATCTTACCGGACAGTGCTGGA----------------------------------------------------	21	-	-	-	-	-	-	-	-	-	1
	-------------------------------------------------------ACACTGTCTGGTAACGATGTT-------------	21	-	-	-	-	-	-	-	-	1	-
	----------------ATCTTACCGGACAGTGCTG------------------------------------------------------	19	-	-	-	-	-	1	-	-	-	-
	----------------------------------------------------------CTGTCTGGTAACGATGTTC------------	19	-	-	-	-	-	-	-	-	-	1
rat	CTGGGCCTCTGTGGGCATCTTACCGGACAGTGCTGGATTTCTTGGCTTGACTCTAACACTGTCTGGTAACGATGTTCAAAGGTGACCCA
human	--------------GCATCTTACCGGACAGTGCTGGATTTCCCAGCTTGACTCTAACACTGTCTGGTAACGATGT--------------
mouse	--------------GCATCTTACCGGACAGTGCTGGATTTCTTGGCTTGACTCTAACACTGTCTGGTAACGATGT--------------
	***************************   *******************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053773 ENSRNOG00000035650 rno-mir-200a
rat	..((((.(((.(((((((((((((((((((((.((((..((.......)).)))).))))))))))))).)))))))).))).).))).	1.000 -42.70
human	((((((((((((((((((((((.....)))))...........)))))))))))).)))))	0.958 -29.40
mouse	((((((((((((((((((.((((..((.......)).)))).))))))))))))).)))))	1.000 -29.40

rat	chromosome:5:172898220:172898308:-1	Same_strand|Exonic_non-coding|ENSRNOT00000053773|ENSRNOG00000035650 ## ENSRNOG00000035650|miRNA|rno-mir-200a|rno-mir-200a [Source:miRBase;Acc:MI0000943] ## {MIR: rno-mir-200a}
human	chromosome:1:1093086:1093214:1	Same_strand|Boundary_non-coding|ENST00000384875|ENSG00000207607|miRNA|hsa-mir-200a [Source:miRBase;Acc:MI0000737] ## {SimpF: oe = 0.62 0 CpG} ## {MIR: hsa-mir-200a}
mouse	chromosome:4:155428986:155429114:-1	Same_strand|Boundary_non-coding|ENSMUST00000051509|ENSMUSG00000029074|protein_coding|tubulin tyrosine ligase-like family, member 10 Gene [Source:MGI (curated);Acc:Ttll10-001] ## Same_strand|Intronic_non-coding|ENSMUST00000097731|ENSMUSG00000029074|protein_coding|tubulin tyrosine ligase-like family, member 10 Gene [Source:MGI (curated);Acc:Ttll10-001] ## {MIR: mmu-mir-200a}

rno-mir-455

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-455 5arm	53	28	41	63	32	82	25	18	47	73
rno-mir-455 3arm	1552	902	1600	923	753	857	921	887	1769	1415
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-455 5arm	0.002	0.001	0.002	0.004	0.002	0.006	0.002	0.001	0.003	0.005
rno-mir-455 3arm	0.052	0.039	0.087	0.055	0.037	0.065	0.072	0.047	0.117	0.094

sblock9754 (miRBase rno-mir-455) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-455

0.001

no

no

0.40/0.67

18/25/0.84

0.0 0.2

0.9 0.1

230 5639

0 0

10 10

0 0

10 9

2 6

5arm 3arm

1 1

nd nd

0.11 0.10

1 1

12041

10

4

4

		reads	miRBase family seed
seed	-------------------------------------------------CAGUCCA-----------------------	7542	novel
seed	--------------------------------------------------AGUCCAC----------------------	3263	novel
seed	-----------------------------------------------UGCAGUC-------------------------	471	novel
seed	-----------AUGUGCC-------------------------------------------------------------	414	miR-455
seed	------------------------------------------------GCAGUCC------------------------	167	novel
seed	----------------------------------------------AUGCAGU--------------------------	130	novel
seed	-------------GUGCCUU-----------------------------------------------------------	28	novel
seed	------------UGUGCCU------------------------------------------------------------	17	novel
seed	---------------------------------------------------GUCCACG---------------------	4	novel
seed	----------UAUGUGC--------------------------------------------------------------	3	novel
seed	---------------------------------------------CAUGCAG---------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------GCAGTCCACGGGCATATACAC----------	21	680	375	374	230	237	330	207	196	714	570
	-------------------------------------------------CAGTCCACGGGCATATACAC----------	20	164	113	247	124	89	34	455	369	228	147
	------------------------------------------------GCAGTCCACGGGCATATACACT---------	22	218	120	336	189	168	158	56	105	276	209
	------------------------------------------------GCAGTCCACGGGCATATAC------------	19	149	89	158	75	65	81	41	58	149	131
	------------------------------------------------GCAGTCCACGGGCATATACA-----------	20	76	49	65	33	36	38	13	22	87	77
	-------------------------------------------------CAGTCCACGGGCATATACACTT--------	22	38	25	113	92	25	34	10	10	51	43
	-------------------------------------------------CAGTCCACGGGCATATACACT---------	21	34	21	125	64	21	14	28	18	57	39
	------------------------------------------------GCAGTCCACGGGCATATA-------------	18	31	21	35	15	19	21	12	20	36	36
	-------------------------------------------------CAGTCCACGGGCATATAC------------	18	18	15	43	29	11	5	37	38	26	14
	-------------------------------------------------CAGTCCACGGGCATATACA-----------	19	17	9	35	23	10	10	26	27	25	7
	----------------------------------------------ATGCAGTCCACGGGCATATAC------------	21	20	14	6	5	20	44	6	8	26	32
rno-miR-455	----------TATGTGCCTTTGGACTACATCG-----------------------------------------------	22	15	14	12	30	9	22	3	4	16	34
	----------------------------------------------ATGCAGTCCACGGGCATATACAC----------	23	27	6	9	4	12	27	5	1	17	19
	----------TATGTGCCTTTGGACTACA--------------------------------------------------	19	11	4	16	10	7	21	8	7	11	10
	-----------------------------------------------TGCAGTCCACGGGCATATACAC----------	22	13	10	4	4	9	17	1	3	21	18
	----------TATGTGCCTTTGGACTACATC------------------------------------------------	21	7	3	8	12	9	10	6	-	6	16
	----------------------------------------------ATGCAGTCCACGGGCATA---------------	18	17	5	6	4	5	5	1	1	10	13
	----------------------------------------------ATGCAGTCCACGGGCATAT--------------	19	9	6	2	4	4	8	4	5	8	13
	---------------------------------------------CATGCAGTCCACGGGCATATAC------------	22	14	3	6	1	4	10	5	-	9	6
	------------------------------------------------GCAGTCCACGGGCATATACACTT--------	23	3	4	10	11	5	5	3	3	4	8
	-----------------------------------------------TGCAGTCCACGGGCATATAC------------	20	8	8	6	2	4	1	1	-	6	4
	----------TATGTGCCTTTGGACTACATCGT----------------------------------------------	23	7	2	1	1	4	4	2	4	5	6
	---------------------------------------------CATGCAGTCCACGGGCATA---------------	19	2	2	2	3	1	5	2	-	4	5
	----------TATGTGCCTTTGGACTAC---------------------------------------------------	18	4	3	1	6	-	6	-	1	3	1
	---------------------------------------------CATGCAGTCCACGGGCATAT--------------	20	6	1	4	-	1	1	1	2	1	3
	---------------------------------------------CATGCAGTCCACGGGCATATACAC----------	24	-	2	1	4	1	2	-	-	2	7
	------------TGTGCCTTTGGACTACATCGTG---------------------------------------------	22	8	-	-	1	1	4	-	-	2	-
	----------------------------------------------ATGCAGTCCACGGGCATATA-------------	20	1	-	1	1	2	2	1	1	1	4
	----------TATGTGCCTTTGGACTACAT-------------------------------------------------	20	-	2	-	1	2	2	2	1	1	1
	-----------------------------------------------TGCAGTCCACGGGCATATACACT---------	23	2	-	2	-	-	1	1	-	4	-
	----------------------------------------------ATGCAGTCCACGGGCATATACACT---------	24	1	-	3	3	-	-	-	-	2	1
	-----------------------------------------------TGCAGTCCACGGGCATAT--------------	18	-	2	-	-	-	-	3	-	-	3
	----------------------------------------------ATGCAGTCCACGGGCATATACA-----------	22	1	2	1	-	2	-	-	-	-	1
	-----------ATGTGCCTTTGGACTACATCGT----------------------------------------------	22	-	-	2	-	-	3	-	-	-	2
	-----------------------------------------------TGCAGTCCACGGGCATATACA-----------	21	-	-	1	2	-	2	-	-	1	-
	-------------------------------------------------CAGTCCACGGGCATATACACTTGC------	24	-	-	2	-	-	-	-	-	-	3
	------------TGTGCCTTTGGACTACATCGT----------------------------------------------	21	-	-	-	-	-	1	4	-	-	-
	-----------ATGTGCCTTTGGACTACA--------------------------------------------------	18	-	-	-	-	-	2	-	-	-	2
	---------------------------------------------CATGCAGTCCACGGGCAT----------------	18	2	-	-	-	1	1	-	-	-	-
	-----------ATGTGCCTTTGGACTACATC------------------------------------------------	20	-	-	-	1	-	2	-	-	1	-
	------------TGTGCCTTTGGACTACATCG-----------------------------------------------	20	-	-	-	-	-	3	-	-	-	-
	--------------------------------------------------AGTCCACGGGCATATACAC----------	19	-	-	1	-	-	-	2	-	-	-
	-----------------------------------------------TGCAGTCCACGGGCATATA-------------	19	-	-	1	-	-	-	-	-	2	-
	------------TGTGCCTTTGGACTACATC------------------------------------------------	19	1	-	-	-	-	-	-	1	1	-
	-----------ATGTGCCTTTGGACTACATCG-----------------------------------------------	21	-	-	-	-	-	2	-	-	-	-
	---------GTATGTGCCTTTGGACTAC---------------------------------------------------	19	-	-	-	1	-	-	-	-	1	-
	---------------------------------------------CATGCAGTCCACGGGCATATACA-----------	23	1	-	-	-	-	-	-	-	-	1
	----------------------------------------------ATGCAGTCCACGGGCATATACACTT--------	25	-	-	-	-	-	-	-	-	2	-
	---------------------------------------------CATGCAGTCCACGGGCATATACACT---------	25	-	-	-	-	-	-	-	-	-	1
	-------------------------------------------------CAGTCCACGGGCATATACACTTG-------	23	-	-	1	-	-	-	-	-	-	-
	------------TGTGCCTTTGGACTACAT-------------------------------------------------	18	-	-	1	-	-	-	-	-	-	-
	--------------------------------------------------AGTCCACGGGCATATACACT---------	20	-	-	-	-	1	-	-	-	-	-
	--------------------------------------------CCATGCAGTCCACGGGCA-----------------	18	-	-	-	-	-	1	-	-	-	-
	---------GTATGTGCCTTTGGACTACA--------------------------------------------------	20	-	-	-	-	-	-	-	-	-	1
	--------------------------------------------CCATGCAGTCCACGGGCATATAC------------	23	-	-	-	1	-	-	-	-	-	-
rat	GGTGTGAGCGTATGTGCCTTTGGACTACATCGTGGACG-CAGCACCATGCAGTCCACGGGCATATACACTTGCCTCAAG
human	------AGGGTATGTGCCTTTGGACTACATCGTGGAAGCCAGCACCATGCAGTCCATGGGCATATACACT---------
mouse	------AGCGTATGTGCCTTTGGACTACATCGTGAACG-CAGCACCATGCAGTCCACGGGCATATACACT---------
	** ************************* * * ***************** *************
	+++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000010333 ENSRNOG00000007657 Col27a1
	+++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042417 ENSRNOG00000007657 Col27a1
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000054389 ENSRNOG00000036266 rno-mir-455
rat	((.(..((.((((((((((.((((((.(((.(((.... ...))).))).)))))).)))))))))).))..).))...	1.000 -37.60
human	...((((((((((.((((((.(((.(((........))).))).)))))).))))))))))...	1.000 -31.10
mouse	...((((((((((.((((((.(((.(((.... ...))).))).)))))).))))))))))...	0.996 -31.00

rat	chromosome:5:80239847:80239924:1	Same_strand|Intronic_coding|ENSRNOT00000042417|ENSRNOG00000007657 ## Same_strand|Exonic_non-coding|ENSRNOT00000054389|ENSRNOG00000036266 ## ENSRNOG00000007657|protein_coding|Col27a1|Collagen alpha-1(XXVII) chain precursor. [Source:UniProtKB/Swiss-Prot;Acc:Q80ZF0] ## ENSRNOG00000036266|miRNA|rno-mir-455|rno-mir-455 [Source:miRBase;Acc:MI0006148] ## {MIR: rno-mir-455}
human	chromosome:9:116011521:116011638:1	Same_strand|Intronic_coding|ENST00000374106|ENSG00000196739|protein_coding|Collagen alpha-1(XXVII) chain Precursor [Source:UniProtKB/Swiss-Prot;Acc:Q8IZC6] ## Same_strand|Boundary_non-coding|ENST00000384993|ENSG00000207726|miRNA|hsa-mir-455 [Source:miRBase;Acc:MI0003513] ## {MIR: hsa-mir-455}
mouse	chromosome:4:62917871:62917988:1	Same_strand|Intronic_coding|ENSMUST00000036300|ENSMUSG00000045672|protein_coding|collagen, type XXVII, alpha 1 Gene [Source:MGI (curated);Acc:Col27a1-001] ## Same_strand|Boundary_non-coding|ENSMUST00000093594|ENSMUSG00000070102|miRNA|mmu-mir-455 [Source:miRBase;Acc:MI0004679] ## {MIR: mmu-mir-455}

miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK (7 loci)

rno-mir-425

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-425 5arm	2114	1768	508	1048	7737	6321	712	1171	1716	2112
rno-mir-425 3arm	234	144	56	74	263	216	53	70	125	154
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-425 5arm	0.070	0.077	0.028	0.062	0.377	0.479	0.055	0.062	0.113	0.141
rno-mir-425 3arm	0.008	0.006	0.003	0.004	0.013	0.016	0.004	0.004	0.008	0.010

sblock12127 (miRBase rno-mir-425) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-425

0.014

no

no

0.48/0.65

18/25/0.52

0.0 0.3

1.9 0.9

12317 730

0 0

10 10

0 0

10 10

4 9

5arm 3arm

1 1

nd nd

0.28 0.22

3 2

26596

10

1

2

Clusters

Located in cluster 83: rno-mir-191, rno-mir-425

		reads	miRBase family seed
seed	-----------AUGACAC-----------------------------------------------------------------	24716	miR-425
seed	----------------------------------------------------UCGGGAA------------------------	791	novel
seed	------------UGACACG----------------------------------------------------------------	428	novel
seed	---------------------------------------------------AUCGGGA-------------------------	378	novel
seed	--------------------------------------------------CAUCGGG--------------------------	168	novel
seed	-----------------------------------------------------CGGGAAU-----------------------	50	novel
seed	-------------GACACGA---------------------------------------------------------------	42	novel
seed	--------------ACACGAU--------------------------------------------------------------	15	novel
seed	---------------CACGAUC-------------------------------------------------------------	3	novel
seed	------------------------------------------------------GGGAAUA----------------------	2	novel
seed	----------AAUGACA------------------------------------------------------------------	2	novel
seed	------------------GAUCACU----------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------AATGACACGATCACTCCC-------------------------------------------------------	18	544	424	148	282	1843	1681	181	318	447	519
rno-miR-425	----------AATGACACGATCACTCCCGTTGA--------------------------------------------------	23	481	427	62	196	1632	1134	170	231	454	469
	----------AATGACACGATCACTCCCG------------------------------------------------------	19	382	306	164	213	1727	1469	131	203	248	387
	----------AATGACACGATCACTCCCGT-----------------------------------------------------	20	353	269	91	164	1216	976	121	178	232	309
	----------AATGACACGATCACTCCCGTTG---------------------------------------------------	22	166	147	12	80	639	404	50	102	138	167
	----------AATGACACGATCACTCCCGTT----------------------------------------------------	21	117	113	14	59	377	361	27	76	92	83
	----------AATGACACGATCACTCCCGTTGAG-------------------------------------------------	24	34	27	8	27	147	174	7	29	37	66
	---------------------------------------------------ATCGGGAATATCGTGTCC--------------	18	60	35	5	11	33	34	15	18	28	40
	---------------------------------------------------ATCGGGAATATCGTGTCCG-------------	19	41	25	15	15	36	28	15	11	21	24
	--------------------------------------------------CATCGGGAATATCGTGTCC--------------	19	31	18	16	18	50	38	4	14	14	15
	----------AATGACACGATCACTCCCGTTGAGT------------------------------------------------	25	9	16	2	10	39	39	4	1	12	22
	---------------------------------------------------ATCGGGAATATCGTGTCCGCCC----------	22	30	14	5	5	27	18	3	8	18	22
	-----------ATGACACGATCACTCCCGTTGA--------------------------------------------------	22	5	15	3	8	34	22	7	8	16	20
	-----------ATGACACGATCACTCCCG------------------------------------------------------	18	11	6	1	3	25	15	7	7	9	21
	---------------------------------------------------ATCGGGAATATCGTGTCCGCC-----------	21	17	10	4	5	14	13	2	3	8	5
	-----------ATGACACGATCACTCCCGT-----------------------------------------------------	19	4	8	-	1	21	12	3	7	9	16
	--------------------------------------------------CATCGGGAATATCGTGTC---------------	18	4	9	3	5	18	19	1	4	3	5
	-------------------------------------------------CCATCGGGAATATCGTGTCCG-------------	21	3	5	3	3	12	13	2	1	5	4
	-------------------------------------------------CCATCGGGAATATCGTGTC---------------	19	2	2	-	1	11	11	1	2	7	3
	-----------ATGACACGATCACTCCCGTTGAG-------------------------------------------------	23	-	2	-	1	9	9	1	-	9	8
	---------------------------------------------------ATCGGGAATATCGTGTCCGC------------	20	9	1	2	1	6	3	1	2	5	7
	-------------------------------------------------CCATCGGGAATATCGTGTCC--------------	20	6	3	3	2	8	8	-	-	2	4
	--------------------------------------------------CATCGGGAATATCGTGTCCGCC-----------	22	2	5	-	-	8	8	1	-	3	2
	--------------------------------------------------CATCGGGAATATCGTGTCCGCCC----------	23	2	5	-	3	5	1	-	-	3	4
	-----------ATGACACGATCACTCCCGTTG---------------------------------------------------	21	2	1	-	-	7	1	1	2	3	6
	-----------ATGACACGATCACTCCCGTT----------------------------------------------------	20	1	2	-	-	9	1	-	4	3	2
	--------------------------------------------------CATCGGGAATATCGTGTCCGC------------	21	1	1	-	1	7	6	2	1	-	3
	-----------ATGACACGATCACTCCCGTTGAGT------------------------------------------------	24	4	-	-	-	1	4	-	1	3	7
	-------------------------------------------------CCATCGGGAATATCGTGT----------------	18	-	3	-	-	4	7	-	-	1	1
	----------------------------------------------------TCGGGAATATCGTGTCCGCCC----------	21	6	1	-	-	3	-	4	-	1	1
	-------------------------------------------------CCATCGGGAATATCGTGTCCGCC-----------	23	3	1	-	-	4	-	1	2	2	2
	--------------------------------------------------CATCGGGAATATCGTGTCCG-------------	20	2	-	-	1	8	1	-	-	-	3
	---------------------------------------------------ATCGGGAATATCGTGTCCGCCCA---------	23	6	1	-	-	1	1	-	-	1	3
	----------------------------------------------------TCGGGAATATCGTGTCCGC------------	19	3	-	-	2	1	1	-	3	-	2
	------------TGACACGATCACTCCCGT-----------------------------------------------------	18	-	-	1	2	-	7	-	1	-	1
	----------------------------------------------------TCGGGAATATCGTGTCCGCCCA---------	22	1	1	-	-	1	3	-	-	1	3
	------------TGACACGATCACTCCCGTTGA--------------------------------------------------	21	1	-	-	-	2	2	1	-	-	4
	------------TGACACGATCACTCCCGTTGAGT------------------------------------------------	23	-	1	-	1	1	2	-	2	1	1
	-------------------------------------------------CCATCGGGAATATCGTGTCCGC------------	22	2	2	-	1	3	-	-	-	-	-
	----------------------------------------------------TCGGGAATATCGTGTCCGCC-----------	20	-	1	-	-	1	2	-	1	-	1
	------------TGACACGATCACTCCCGTTG---------------------------------------------------	20	-	-	-	-	3	2	-	-	-	-
	----------------------------------------------------TCGGGAATATCGTGTCCG-------------	18	-	1	-	-	2	-	1	-	1	-
	------------TGACACGATCACTCCCGTTGAG-------------------------------------------------	22	-	-	-	-	2	2	-	-	1	-
	-------------GACACGATCACTCCCGTTGAGT------------------------------------------------	22	-	-	-	-	-	-	1	-	1	2
	-------------GACACGATCACTCCCGTT----------------------------------------------------	18	-	3	-	-	-	1	-	-	-	-
	-------------GACACGATCACTCCCGTTG---------------------------------------------------	19	-	1	-	-	1	2	-	-	-	-
	-------------------------------------------------CCATCGGGAATATCGTGTCCGCCC----------	24	1	-	-	-	-	1	-	-	-	-
	-------------GACACGATCACTCCCGTTGAG-------------------------------------------------	21	-	-	-	-	-	1	-	-	1	-
	--------------ACACGATCACTCCCGTTGAGTG-----------------------------------------------	22	-	-	2	-	-	-	-	-	-	-
	---------GAATGACACGATCACTCCC-------------------------------------------------------	19	-	-	-	-	1	-	-	-	-	1
	-----------------CGATCACTCCCGTTGAGT------------------------------------------------	18	-	-	-	-	1	-	-	-	-	-
	-------------GACACGATCACTCCCGTTGA--------------------------------------------------	20	-	-	-	-	-	-	-	-	-	1
	--------------ACACGATCACTCCCGTTG---------------------------------------------------	18	-	-	-	1	-	-	-	-	-	-
	----------------------------------------------------TCGGGAATATCGTGTCCGCCCAGT-------	24	-	-	-	-	-	-	-	-	1	-
	-----------------------------------------------------CGGGAATATCGTGTCCGCC-----------	19	1	-	-	-	-	-	-	-	-	-
	-----------------------------------------------------CGGGAATATCGTGTCCGCCC----------	20	1	-	-	-	-	-	-	-	-	-
	------------TGACACGATCACTCCCGTT----------------------------------------------------	19	-	-	-	-	-	-	-	1	-	-
rat	AGTGCTTTGGAATGACACGATCACTCCCGTTGAGTGGGCACCCAAGAAGCCATCGGGAATATCGTGTCCGCCCAGTGCTCTTT
human	----------AATGACACGATCACTCCCGTTGAGTGGGCACCCGAGAAGCCATCGGGAATGTCGTGTCCGC------------
mouse	----------AATGACACGATCACTCCCGTTGAGTGGGCACCCAAGAAGCCATCGGGAATGTCGTGTCCGC------------
	********************************* **************** **********
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....	ENSRNOT00000053607 ENSRNOG00000035484 rno-mir-425
rat	((.((.((((...((((((((...(((((.((..(((....)))......)).)))))..))))))))...)))).)).))..	1.000 -30.70
human	...(((((((.((.(((((.((..(((....)))......)).))))).)))))))))...	0.454 -23.90
mouse	...(((((((.((.(((((.((..(((....)))......)).))))).)))))))))...	1.000 -24.60

rat	chromosome:8:113614817:113614899:1	Same_strand|Exonic_non-coding|ENSRNOT00000053607|ENSRNOG00000035484 ## ENSRNOG00000035484|miRNA|rno-mir-425|rno-mir-425 [Source:miRBase;Acc:MI0006146] ## {MIR: rno-mir-425}
human	chromosome:3:49032566:49032688:-1	Same_strand|Boundary_non-coding|ENST00000395462|ENSG00000178149|protein_coding|DALR anticodon-binding domain-containing protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5D0E6] ## Same_strand|Intronic_non-coding|ENST00000313778|ENSG00000178149|protein_coding|DALR anticodon-binding domain-containing protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5D0E6] ## {SimpF: oe = 0.78 0 CpG,rank = 2 1 FirstEF} ## {MIR: hsa-mir-425}
mouse	chromosome:9:108471090:108471212:1	Same_strand|Boundary_non-coding|ENSMUST00000083645|ENSMUSG00000065579|miRNA|mmu-mir-425 [Source:miRBase;Acc:MI0001447] ## {MIR: mmu-mir-425}

rno-mir-375

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-375 5arm	0	1	0	0	3	2	0	0	1	1
rno-mir-375 3arm	52	49	90	160	193	483	0	0	116	180
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-375 5arm	0	0.000	0	0	0.000	0.000	0	0	0.000	0.000
rno-mir-375 3arm	0.002	0.002	0.005	0.009	0.009	0.037	0	0	0.008	0.012

sblock12235 (miRBase rno-mir-375) [miRNAknown_lenNOK_cloningHIGH_multiarm_DicerOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

miRBase rno-mir-375

0.088

no

no

0.52/0.78

18/23/0.46

0.0 0.0

1.6 1.1

8 608

0 0

5 8

0 0

9 9

1 3

5arm 3arm

1 1

nd nd

0.26 0.22

3 3

1331

8

2

2

		reads	miRBase family seed
seed	---------------------------------------------------------UUGUUCG-------------------------	1258	miR-375
seed	----------------------------------------------------------UGUUCGU------------------------	59	novel
seed	----------------------CGACGAG------------------------------------------------------------	8	novel
seed	--------------------------------------------------------UUUGUUC--------------------------	3	novel
seed	-----------------------------------------------------------GUUCGUU-----------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T5S1	T5S2
	--------------------------------------------------------TTTGTTCGTTCGGCTCGC---------------	18	23	20	32	62	96	193	54	83
rno-miR-375	--------------------------------------------------------TTTGTTCGTTCGGCTCGCGTGA-----------	22	11	11	28	44	44	174	38	41
	--------------------------------------------------------TTTGTTCGTTCGGCTCGCG--------------	19	5	4	12	20	17	37	6	29
	--------------------------------------------------------TTTGTTCGTTCGGCTCGCGT-------------	20	7	4	11	17	17	37	6	8
	--------------------------------------------------------TTTGTTCGTTCGGCTCGCGTG------------	21	5	7	-	10	9	20	4	5
	---------------------------------------------------------TTGTTCGTTCGGCTCGCGTGA-----------	21	1	2	5	2	6	11	5	5
	---------------------------------------------------------TTGTTCGTTCGGCTCGCG--------------	18	-	-	1	-	1	4	1	2
	---------------------------------------------------------TTGTTCGTTCGGCTCGCGT-------------	19	-	-	-	2	1	1	1	2
	--------------------------------------------------------TTTGTTCGTTCGGCTCGCGTGAG----------	23	-	-	1	1	-	4	-	1
	---------------------GCGACGAGCCCCTCGCACAAACC---------------------------------------------	23	-	1	-	-	3	-	-	1
	---------------------------------------------------------TTGTTCGTTCGGCTCGCGTG------------	20	-	-	-	1	2	-	-	1
	---------------------GCGACGAGCCCCTCGCACA-------------------------------------------------	19	-	-	-	-	-	2	-	-
	-------------------------------------------------------TTTTGTTCGTTCGGCTCGC---------------	19	-	-	-	1	-	-	1	-
	---------------------------------------------------------TTGTTCGTTCGGCTCGCGTGAG----------	22	-	1	-	-	-	-	-	1
	----------------------------------------------------------TGTTCGTTCGGCTCGCGTGA-----------	20	-	-	-	-	-	1	-	1
	----------------------------------------------------------TGTTCGTTCGGCTCGCGTG------------	19	-	-	-	-	-	-	-	1
	---------------------GCGACGAGCCCCTCGCAC--------------------------------------------------	18	-	-	-	-	-	-	1	-
	-------------------------------------------------------TTTTGTTCGTTCGGCTCGCGT-------------	21	-	-	-	-	-	1	-	-
rat	------------TCCGGCCCCGCGACGAGCCCCTCGCACAAACCGGACCTGAGCGTTTTGTTCGTTCGGCTCGCGTGAGGCAGGGGC--
human	CGGGCCCTCCGCTCCCGCCCCGCGACGAGCCCCTCGCACAAACCGGACCTGAGCGTTTTGTTCGTTCGGCTCGCGTGAGGCAGGGGCG-
mouse	--------CCGCTCCGGCCCCGCGACGAGCCCCTCGCACAAACCGGACCTGAGCGTTTTGTTCGTTCGGCTCGCGTGAGGCAGGGGCGG
	*** ***********************************************************************
	.....            >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  .....	ENSRNOT00000053578 ENSRNOG00000035455 rno-mir-375
rat	(((.(((.((((.((((((...((.(((((.((........)).))))).))...)))))))))).))).)))..	1.000 -33.80
human	.........((((((.(((.((((.((((((...((.(((((.((........)).))))).))...)))))))))).))).))))))	0.910 -41.70
mouse	(((((((.(((.((((.((((((...((.(((((.((........)).))))).))...)))))))))).))).)))))))	0.996 -44.70

rat	chromosome:9:74233499:74233573:-1	Same_strand|Boundary_non-coding|ENSRNOT00000053578|ENSRNOG00000035455 ## Same_strand|Exonic_non-coding|ENSRNOT00000053578|ENSRNOG00000035455 ## ENSRNOG00000035455|miRNA|rno-mir-375|rno-mir-375 [Source:miRBase;Acc:MI0006140] ## {SimpF: -1 Eponine} ## {MIR: rno-mir-375}
human	chromosome:2:219574604:219574691:-1	Same_strand|Boundary_non-coding|ENST00000362103|ENSG00000198973|miRNA|hsa-mir-375 [Source:miRBase;Acc:MI0000783] ## {SimpF: oe = 0.73 0 CpG, -1 Eponine} ## {MIR: hsa-mir-375}
mouse	chromosome:1:74947224:74947304:-1	Same_strand|Boundary_non-coding|ENSMUST00000083682|ENSMUSG00000065616|miRNA|mmu-mir-375 [Source:miRBase;Acc:MI0000792] ## {SimpF: oe = 0.84 -1 CpG, -1 Eponine} ## {MIR: mmu-mir-375}

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candidate miRBase miRNAs:

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